Stayin' Alive - Covid-19 #10

[Wilbur]

Enjoy this (sumo-centric) summary of the situation in Japan:

Japan's state of emergency

[The Anti-Targ]

 

5 hours ago, Fury Resurrected said:

I hyperdose vitamin D (20,000 iu first month then 10,000iu thereafter) from October to May for SAD and it does nothing at all to keep me from getting all the cold and flu symptoms everyone else does.

Different people are different. But the science tells us that people with sufficient vitamin D have better functioning immune systems than people in Vitamin D deficit. I don't know enough about SAD to know if people who have if have underlying issues with their immune systems, but if Vit D is part of the therapy it implies there's some immune system element to it.

[mcbigski]

On 4/8/2020 at 8:53 AM, Toth said:

Well, thanks and you are right, it is likely my posture. I am working with my laptop, but I have put it on a wooden stand and am using an ergonomic mouse to limit the stress on my hand. I am also sitting at a desk with a decent chair, but unfortunately I am sharing that one with my mother and when it is blocked I have to retreat onto my bed, which is literally suicide and it's my own fault for doing that.

For me, it's sitting down too much that makes my back hurt.  The cure for me is squats and deadlifts.  Put your body through a full range of motion.  Not that you can test that easily right now alas.  Over the last year or two I kept thinking I should turn my otherwise underused basement room into a home gym.  And now the places I would go to buy a rack, weights, flooring, bars etc are closed as non-essential, I think.

On 4/8/2020 at 3:10 PM, Ran said:

Everyone will be Sweden at some point or other, except for those few nations (mostly islands like Taiwan, Singapore, NZ, Japan, or countries with only one or two borders to concern themselves with) which can feasibly slow outside vectors to a trickle until a vaccine exists. This would include quarantine of citizens whenever they return from trip abroads, quarantining visitors, etc.

It’ll kill tourism and harm adjacent sectors, but depending on how much that matters to the country, maybe that’s a fair price to pay. 

I think the US should go there sooner rather than later.  If you have some sort of complication where Covid will compound your issues, then stay isolated.  If you have symptoms or have been exposed to someone who has been verified and you're awaiting your test, stay isolated.  But if you're in a low risk classification, go and work, and still be cautious.   But the idea that everyone can stay at home for three weeks without starving is a kind of ambitious. 

Do you think Sweden's approach is working for Sweden?  Could it work elsewhere?  Not everywhere in the US is New York or New Orleans.  One size probably shouldn't fit all here.symptoms everyone else does.

 

Found this interesting

https://chemrxiv.org/articles/COVID-19_Disease_ORF8_and_Surface_Glycoprotein_Inhibit_Heme_Metabolism_by_Binding_to_Porphyrin/11938173

Being a Chinese source, I'm assuming it's translated, so jargon plus translation.  But again, it sounds like the virus attacks red blood cells more directly than lungs.

(would explain why bilateral pneumonia is far more common with Covid - the blood gets even distributed thoughout the lungs and if the hemoglobin gets damaged then all lung tissue gets fucked at once.)

Makes me think that maybe AOC is right about this one (stopped clock...and not for the reasons she would correct for).  If Covid affects hemoglobin it could very well have a higher impact on people with sickle cell trait.  Some doctors have described it as more like an altitude sickness gone excessive. 

Making some barely at best supported conjectures here, but if it does attack the blood, and does impact people who are genetically predisposed to carry less oxygen in the blood as a defense against malaria, maybe anti malaria drugs could be beneficial.  (and not just because POTUS owns about 2 shares of a company than manufactures that generic drug).

Sadly, since everything is politicized these days, it will probably take several generations for the actual facts to applied to the next pandemic, alas.

 

[ithanos]

40 minutes ago, mcbigski said:

Found this interesting

https://chemrxiv.org/articles/COVID-19_Disease_ORF8_and_Surface_Glycoprotein_Inhibit_Heme_Metabolism_by_Binding_to_Porphyrin/11938173

Being a Chinese source, I'm assuming it's translated, so jargon plus translation.  But again, it sounds like the virus attacks red blood cells more directly than lungs.

(would explain why bilateral pneumonia is far more common with Covid - the blood gets even distributed thoughout the lungs and if the hemoglobin gets damaged then all lung tissue gets fucked at once.)

Makes me think that maybe AOC is right about this one (stopped clock...and not for the reasons she would correct for).  If Covid affects hemoglobin it could very well have a higher impact on people with sickle cell trait.  Some doctors have described it as more like an altitude sickness gone excessive. 

Making some barely at best supported conjectures here, but if it does attack the blood, and does impact people who are genetically predisposed to carry less oxygen in the blood as a defense against malaria, maybe anti malaria drugs could be beneficial.  (and not just because POTUS owns about 2 shares of a company than manufactures that generic drug).

Sadly, since everything is politicized these days, it will probably take several generations for the actual facts to applied to the next pandemic, alas.

 

Interesting indeed, thanks for sharing it. Emphasis mine.

To quote from the link...

Quote

Since the ability of chloroquine to inhibit structural proteins is not particularly obvious, the therapeutic effect on different people may be different. 

but ofcourse, 

Quote

Due to the side effects and allergic reactions of drugs such as chloroquine, please consult a qualified doctor for treatment details, and do not take the medicine yourself.

 

[Ran]

56 minutes ago, mcbigski said:

Do you think Sweden's approach is working for Sweden?

I do, to a point -- one of the stated objectives has partially failed, namely that this has spread into some of the rest homes in Sweden, particularly Stockholm when one of the goals was to protect them. But this has also happened in Denmark, which closed up much tighter than we did, and even Norway to a lesser degree, which is the tightest of the three. Part of our demographic structure is that the elderly live alone or in rest homes, rather than in multigenerational families, and in theory this means if we can quarantine them from the disease while herd immunity is established in the less vulnerable population, we'd get out the other side relatively fine. But if we can't quarantine them, it means it gets to run rampant through those groups.

Quote

  Could it work elsewhere? 

I do think it can, but the Swedish approach is shaped to particular aspects of Swedish society, such as having more than 50% of all households being single person. I don't know the statistics in the US for that. OTOH, the US tends to have more ICU beds, so in theory places that aren't quite so dense -- suburban areas, smaller cities, rural communities, etc. -- could feasibly mostly just carry on with restrictions on large gatherings, public venues, etc. and focus on protecting risk groups better.

Quote

Not everywhere in the US is New York or New Orleans.  One size probably shouldn't fit all here.

I think that's true. So long as you can find a balance between overburderning health care resources and underutilizing them, various states/counties/municipalities could create plans to fit. OTOH, the structure of US government -- federal as an overarching layer, then state, county, municipal -- adds layers of complexity. How granular you want to get also has to recognize the fact that people move around. If, say, Minneapolis closes down all bars because of an outbreak, and St. Paul keeps them open, this is just going to cause problems as people from Minneapolis go over to St. Paul. That sort of thing.

 

[Guest]

7 minutes ago, Ran said:

I do, to a point -- one of the stated objectives has partially failed, namely that this has spread into some of the rest homes in Sweden, particularly Stockholm when one of the goals was to protect them. But this has also happened in Denmark, which closed up much tighter than we did, and even Norway to a lesser degree, which is the tightest of the three. Part of our demographic structure is that the elderly live alone or in rest homes, rather than in multigenerational families, and in theory this means if we can quarantine them from the disease while herd immunity is established in the less vulnerable population, we'd get out the other side relatively fine. But if we can't quarantine them, it means it gets to run rampant through those groups.

I do think it can, but the Swedish approach is shaped to particular aspects of Swedish society, such as having more than 50% of all households being single person. I don't know the statistics in the US for that. OTOH, the US tends to have more ICU beds, so in theory places that aren't quite so dense -- suburban areas, smaller cities, rural communities, etc. -- could feasibly mostly just carry on with restrictions on large gatherings, public venues, etc. and focus on protecting risk groups better.

I think that's true. So long as you can find a balance between overburderning health care resources and underutilizing them, various states/counties/municipalities could create plans to fit. OTOH, the structure of US government -- federal as an overarching layer, then state, county, municipal -- adds layers of complexity. How granular you want to get also has to recognize the fact that people move around. If, say, Minneapolis closes down all bars because of an outbreak, and St. Paul keeps them open, this is just going to cause problems as people from Minneapolis go over to St. Paul. That sort of thing.

 

I think the U.S. again suffers from the special snowflake problem. Outside of the elderly/retired, the most at-risk groups are always going to be the ones classified as essential, have the fewest protections like sick leave, are the least likely to have insurance, and among the most likely to get infected.

[Toth]

Ah shit. Yesterday my principal sent a mail around that everybody who is in the high risk group needs to send in some kind of proof till next Wednesday. And since I saw that only late in the night I had no chance to call my lung specialist whether my Asthma is considered that. My asthma is so soft that I never had any problems whatsoever with it despite my unhealthy avoidance of all kinds of sports. And now  I read that lung specialist is in easter holidays anyway, so I can't ask her until two days after I have to turn this in...

Shit... I also must admit that my first reflex was to just not say anything, because I have started my job only last semester and this would make me look bad if I put my completely harmless Asthma forward to get out of my responsibilities... This whole thing is unnecessarily nervewracking...

[Impmk2]

1 hour ago, mcbigski said:

Found this interesting

https://chemrxiv.org/articles/COVID-19_Disease_ORF8_and_Surface_Glycoprotein_Inhibit_Heme_Metabolism_by_Binding_to_Porphyrin/11938173

Being a Chinese source, I'm assuming it's translated, so jargon plus translation.  But again, it sounds like the virus attacks red blood cells more directly than lungs.

 

It's entirely in-silco work (ie computer modelling) so should be taken with an absolutely massive grain of salt. This stuff is worth following up on, but you can never trust it until you see it backed up experimentally.

[Ran]

37 minutes ago, The Great Unwashed said:

I think the U.S. again suffers from the special snowflake problem. Outside of the elderly/retired, the most at-risk groups are always going to be the ones classified as essential, have the fewest protections like sick leave, are the least likely to have insurance, and among the most likely to get infected.

Yes, that's another issue that makes it hard to say what is best for the US in the main.

[RhaenysBee]

Whoa. 210 new cases today. About 150ish of that is within ONE old people’s home, that has become a critical epicenter in the past few days. As far as I know, they tested everybody in the facility, or at least testing, but I’m not sure what else was done to contain it and how much people will actually work on that over the holidays. Now the lack to further restrictions seems even more dangerous. 

[Isis]

On 4/9/2020 at 10:29 AM, Chaircat Meow said:

In the UK we think the first cases may have been mid-January as people came back from Alpine ski resorts. can't find link to the story at the moment.

Oddly enough half of my office, including me, had moderate to bad flu in early-mid February and we are in central London (I lived in London's COVID-19 hotspot at the time, Southwark.) No one really thought it was Corona but it might have been as flu never seemed to hit so many people so hard in previous years. As most people are under-40 it may have been able to spread around the office without causing a serious case. On the other hand, may just have been the usual. 

"Moderate to bad flu" means what to you? Being bed-ridden for 7-10 days is standard for influenza. Like, you can barely manage trips to the bathroom. You seem to be saying that you/your colleagues think you are getting flu every year? The flu isn't a cold. Even though some colds are very bad and hang around a long time (about five years back, many of my colleagues had a cold in January (NOT the flu!) which lasted for a good couple of weeks, with headaches/body aches, sinus pain etc) but we were able to come into work after a few days. Getting 'a touch of flu'  is not a thing really - it's an infection which knocks you down for weeks (until you get back to full health) not days. It's not likely that multiple people in one office get the flu every year. The figures do not bear this out. I've had flu twice in my life (age 18 and 24). 

Could it have been COVID-19 making you and your colleagues sick? Yes, of course it. Exposures were high in London.

23 hours ago, Rippounet said:

So 11,000 deceased in France.
Since I've been following the numbers these last few days it seems we're not far from 1,000/day.

There's a rumor that "patient zero" in France was aboard a specially chartered plane (a military A340 to be specific) bringing back VIPs (business people, diplomats...) from Wuhan on January 31.
Having checked, it seems to be bullshit. The people were all quarantined and under medical surveillance, and on January 31 France had already 6 cases of Covid-19.

 

Yes, the first positive tested case in France was on January 24th.

21 hours ago, Rippounet said:

So, just to be clear, what we're starting to see is that:

- Most Covid-19 patients are asymptomatic. This isn't a surprise really, and it's good news since we'll move faster to herd immunity than was expected (by many experts at least)

By that you suggest that >50% of positive cases have no symptoms. I have not seen, read or heard that anywhere. Some studies have said up to 50%. In the UK, the Chief Scientific Advisor said last night that they don't know, but it could be 20% or 30%. So bottom line, it's not 'most people'.

18 hours ago, Mudguard said:

As I mentioned before, the modeling is very unreliable for numerous factors.  If you've been following some of the Imperial Colleges modelling, the predictions can change by orders of magnitude week to week.  A massive shift in their model's prediction is what caused Britain to go from light mitigation to lockdown.  Same thing with the US models.  Massive changes in predictions week to week.

Also, I would not trust any antibody testing to accurately report low rates of infection due to the problem of false positives. In the US, we recently approved an antibody test for emergency use only (not for diagnostic use by itself, but only in conjunction with other testing), and it has around 95% sensitivity and 95% specificity.  That means about 5% false negative and 5% false positive.  Sounds OK?  Depends on what you want to do.  If 0.1% of the population is actually infected, that antibody test is still going to identify about 5% of the population as infected, with virtually all being false positives.  Britain was claiming that they would have an antibody test soon, but they backtracked after actually testing the performance.  So going back to the Denmark antibody test, if the sensitivity of the test was 96.5%, that test would tell you that at least around 3.5% of the population was positive, even if the actual percentage was around 0.1%.  I'd need to see that their antibody test was properly validated, and not just based on the claimed sensitivity by the manufacturer.  Many manufacturers are claiming 100% sensitivity (0% false positives), but I'm extremely skeptical of those claims.  It's either based on extremely limited testing, or outright fabrication.  

Models change when you change the values you put into them, yes. The 'science' didn't change re the models from LSHTM and Imperial. What was happening in Italy made them realise that more people were going to require hospitalisation. That meant that mitigation was not an option as the NHS ICU capacity would be overwhelmed by mid-April.

Interested to know what you mean by an antibody test for emergency use. You are correct when you say that sensitivity and specificity values matter depending on how you want to use the tests. Context is everything when selecting the appropriate test. What they should be doing is using (at least) two tests. One to screen (high sensitivity) and one to confirm (high specificity). This is the standard approach in ref labs doing serology tests. The manufacturer's claims, in this context, will be in peer reviewed papers - that's what you see in the kit inserts, so you can check all the refs for yourself. Ok, this may be a language/terminology thing, but in the UK verification and validation have specific meanings in diagnostic labs. Verification is when you use a commercial assay but you show that it gives you the results you would expect in your lab, with your staff, equipment etc - i.e. it is fit for purpose. Validation is where you (a lab) provide evidence that a new test does what you expect it to do (this requires much more data). And whatever terms we use, yes, we need for labs doing clinical testing to be able to show that a given test works in their hands.

But I think your discussion on seemingly low sens and spec values is not really appropriate here.There is no perfect test!   Those are not unusual values for commercial tests. It comes back to how are you using those tests. You choose the right test for the right scenario at the right time, i.e. let the experts do their job.

17 hours ago, Mudguard said:

If the specificity is actually only about 98%, the test would report that 2% of the population is positive even if the real percentages is zero.

Yes. This is normal and happens for many other diseases. 

17 hours ago, Mudguard said:

We shall see.  Validation would require testing against a panel of common coronaviruses, other types of viruses, and hundreds of blood or plasma samples from early 2019 or earlier.  It's possible for an academic lab to do this, but it would be difficult.

It will be possible for virology reference centres, who will have positive material which they use for controls etc. That's part of their job.

16 hours ago, Mudguard said:

Generally speaking, all the antibody tests are ELISA tests, and should be very rapid, at least when compared to RT-PCR methods.  The Heinsburg study test should be similar to all the other tests in structure and methodology (there's two different types of structure for the test, which depends on whether you immobilize an antibody or antigen on the testing substrate).  Where the design comes in that differentiates all these antibody tests is what antigen (or antibody) is immobilized on the substrate. 

How long does an ELISA take? About two hours. How long does real-time PCR take? About two hours.

 

[Rippounet]

1 hour ago, Isis said:

By that you suggest that >50% of positive cases have no symptoms. I have not seen, read or heard that anywhere. Some studies have said up to 50%. In the UK, the Chief Scientific Advisor said last night that they don't know, but it could be 20% or 30%. So bottom line, it's not 'most people'.

Uh, my bad. My brain indeed fethed up the numbers.

So it seems we're talking about 12,000 dead in France now, which (if I've been following this right) does come close to 1,000 dead per day.
And we haven't even reached the peak of the curve just yet. We also have about 7,000-8,000 people in ICU atm.

In other news:
- Macron has visited Raoult.
- Sanofi is promising 100M doses of hydroxychloroquine (Plaquenil) - to be distributed worldwide for free, as a I understand it, though I doubt it's really going to be "free." But Sanofi did warn that the drug is not proved to be a cure and that is has serious side effects. And meanwhile...
- People have already died due to those side effects. I'm reading 54 cases of heart problems with 4 dead for France alone.

I know thinking about a "cure" is a way to cope with anxiety, but I wish the media would stop spending so much time on chloroquine and move on to other leads or updates...

[Raja]

Yeah - when I read those figures in the previous few posts, I was also curious re: asymptomatic people. There's a lot of different research out there ( some of it not that great), this website here compiles it all together in a easy to read table - I'd be curious to read the Iceland numbers properly but I can't find the results of that study.

Part of this is acknowledging what you do & don't know, here's the conclusion based on the papers they looked at - honestly surprised there hasn't  been a meta-analysis on this yet, but I'm sure there will be

Quote

We also learnt that there  is not a single reliable study to determine the number of  asymptotics. It is likely we will only learn the true extent once population based antibody testing  is undertaken.

There's a temptation in these threads to make broad conclusions based on very little science, which we should all be wary of doing.

 

[williamjm]

5 hours ago, Toth said:

Ah shit. Yesterday my principal sent a mail around that everybody who is in the high risk group needs to send in some kind of proof till next Wednesday. And since I saw that only late in the night I had no chance to call my lung specialist whether my Asthma is considered that. My asthma is so soft that I never had any problems whatsoever with it despite my unhealthy avoidance of all kinds of sports. And now  I read that lung specialist is in easter holidays anyway, so I can't ask her until two days after I have to turn this in...

Shit... I also must admit that my first reflex was to just not say anything, because I have started my job only last semester and this would make me look bad if I put my completely harmless Asthma forward to get out of my responsibilities... This whole thing is unnecessarily nervewracking...

Can you say this to your principal that you're waiting for a reply from your specialist and that may not be until after the deadline? That would seem better than saying nothing.

22 minutes ago, Raja said:

Yeah - when I read those figures in the previous few posts, I was also curious re: asymptomatic people. There's a lot of different research out there ( some of it not that great), this website here compiles it all together in a easy to read table - I'd be curious to read the Iceland numbers properly but I can't find the results of that study.

Part of this is acknowledging what you do & don't know, here's the conclusion based on the papers they looked at - honestly surprised there hasn't  been a meta-analysis on this yet, but I'm sure there will be

There's a temptation in these threads to make broad conclusions based on very little science, which we should all be wary of doing.

The Internet is a great tool for finding information but it does have the disadvantage that people will end up hailing new breakthroughs or panicking about new disasters based on a twitter post about a newspaper article about a study which hasn't yet been peer-reviewed.

[Toth]

12 minutes ago, williamjm said:

Can you say this to your principal that you're waiting for a reply from your specialist and that may not be until after the deadline? That would seem better than saying nothing.

Well, I have searched the internet and seen several statements from some kind of lung doctor guild that as long as you are properly medicated (which I am), don't show any Asthma symptoms (what I don't) and you are below the age threshold (which I am), you aren't necessarily more at risk than anyone else. I wrote her a quick mail this morning stating this much and that I think with the appropriate safety measures I will be fine, but that I don't know for sure until Monday after the next when my lung doctor is back.

[Chaircat Meow]

4 hours ago, Isis said:

"Moderate to bad flu" means what to you? Being bed-ridden for 7-10 days is standard for influenza. Like, you can barely manage trips to the bathroom. You seem to be saying that you/your colleagues think you are getting flu every year? The flu isn't a cold. Even though some colds are very bad and hang around a long time (about five years back, many of my colleagues had a cold in January (NOT the flu!) which lasted for a good couple of weeks, with headaches/body aches, sinus pain etc) but we were able to come into work after a few days. Getting 'a touch of flu'  is not a thing really - it's an infection which knocks you down for weeks (until you get back to full health) not days. It's not likely that multiple people in one office get the flu every year. The figures do not bear this out. I've had flu twice in my life (age 18 and 24). 

Could it have been COVID-19 making you and your colleagues sick? Yes, of course it. Exposures were high in London.

I don't know - not good at telling colds and flu apart. Some of the people I was talking about did have the bolded yes. I didn't have it that bad - I was in bed for about three days. That may be because it wasn't the same thing I suppose. 

[Guest]

2 hours ago, Toth said:

Well, I have searched the internet and seen several statements from some kind of lung doctor guild that as long as you are properly medicated (which I am), don't show any Asthma symptoms (what I don't) and you are below the age threshold (which I am), you aren't necessarily more at risk than anyone else. I wrote her a quick mail this morning stating this much and that I think with the appropriate safety measures I will be fine, but that I don't know for sure until Monday after the next when my lung doctor is back.

Are the medications you take for your asthma steroidal? My son has (a more severe form of) asthma also, and he's considered high-risk because of the asthma and the immunosuppressive effects of steroids.

[Guest]

6 hours ago, Isis said:

"Moderate to bad flu" means what to you? Being bed-ridden for 7-10 days is standard for influenza. Like, you can barely manage trips to the bathroom. You seem to be saying that you/your colleagues think you are getting flu every year? The flu isn't a cold. Even though some colds are very bad and hang around a long time (about five years back, many of my colleagues had a cold in January (NOT the flu!) which lasted for a good couple of weeks, with headaches/body aches, sinus pain etc) but we were able to come into work after a few days. Getting 'a touch of flu'  is not a thing really - it's an infection which knocks you down for weeks (until you get back to full health) not days. It's not likely that multiple people in one office get the flu every year. The figures do not bear this out. I've had flu twice in my life (age 18 and 24). 

Could it have been COVID-19 making you and your colleagues sick? Yes, of course it. Exposures were high in London.

I was under the impression that a cold is a milder form of upper/lower respiratory infection that specifically presents without a fever, and that a moderate respiratory infection with fever was more likely to be the flu (I think I've only ever actually been tested for flu once - came back negative).

ETA: Not saying that as in a "you're wrong" way. More of a "my doctors have been bullshitting me this whole time?!?!" way.

[Guest]

8 hours ago, Ran said:

Yes, that's another issue that makes it hard to say what is best for the US in the main.

Yep, we always have to make shit difficult.

I think it's increasingly likely that people will realize that the U.S. needs to massively expand it's social safety net. The only question in my view is whether that expansion comes about via a progressive implementation, or a nationalist one.

[Toth]

12 minutes ago, The Great Unwashed said:

Are the medications you take for your asthma steroidal? My son has (a more severe form of) asthma also, and he's considered high-risk because of the asthma and the immunosuppressive effects of steroids.

I take Beclometasone daily and it is specifically noted in several articles and interviews I have read that asthma sprays containing this don't make you high risk (despite the side effects list stating otherwise, but oh well...), instead heavier dosages that are done to combat severe Asthma are. Then again, I am just a layman. I rather don't want to make a statement this strong without the judgement of my doctor.